- Sliding Ghost
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Their fear of the Prophets was greater than their fear of the Arbiter. May Arbiter's vengeance rightly come upon them.
But seriously, it's because the Hunters had concerns about their home world and the Grunts were scared into submission by the Brutes. Notice there aren't many Hunter encounters in Halo 3.
Imo, I think it's because of the story. The exclusion of Zealots. The exclusion of Ultra Elites. This is not about the Covenant separatists. It's about the UNSC. We're seeing things from the UNSC perspective. Covie Separatists got sidelined with Arbiter making the only significant appearance.